Hellooo, somebody from Apple!
Apple rarely posts any responses in the forum, which is meant for user to user support, and probably has not even have seen your question. You will either need to use AppleCare, visit a Genius bar or send feedback to get an answer from Apple.
This is still happening for me in 10.9.3. Every time I download or save something, it rearranges my icons in the Downloads folder. I was blaming Default Folder X, especially since my Documents folder kept doing it too even when it wasn't the destination of the save or download (Documents is it's default save folder), but I tried disabling that and even uninstalling. Problem persists. Tried on a work computer without it, same issue. Was blaming FireFox too, but it also happens in Safari, TextEdit, and Word from what I can tell. Others maybe too, but that's what I save from. As long as that Save Window pops up, the folder reverts to default view. Doesn't happen when Safari is set to automatically download to a subfolder in Downloads though.
Tried fixing permissions mutliple times, reseting that folders settings after deleting the .DS_Store, reseting the Finder's settings, even deleting ALL .DS-Store files via Onyx. Still reverts back. I even tried a trick that had worked in the past where you show all hidden files, manually delete the .DS_Store, change the view settings, then lock the new .DS_Store thats recreated. Rebooted, seemed to work, resets again when I download or save. Nothing works. Getting frustrating Apple. Support did nothing to help me, so I'm hoping it's a bug that someone eventually fixes. Given how old these threads are and that it still keeps popping up though... doubtful.